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Deep learning-guided selection of antibody therapies with enhanced resistance to current and prospective SARS-CoV-2 Omicron variants
(2023)bioRxivMost COVID-19 antibody therapies rely on binding the SARS-CoV-2 receptor binding domain (RBD). However, heavily mutated variants such as Omicron and its sublineages, which are characterized by an ever increasing number of mutations in the RBD, have rendered prior antibody therapies ineffective, leaving no clinically approved antibody treatments for SARS-CoV-2. Therefore, the capacity of therapeutic antibody candidates to bind and neutralize ...Working Paper -
The Robotic Herd: Using Human-Bot Interactions to Explore Irrational Herding
(2023)SocArXivWe explore human herding in a strategic setting where humans interact with automated entities (bots) and study the shift in the behavior and beliefs of humans when they are aware of interacting with bots. The strategic setting is an online minority game, where 1,997 participants are rewarded for following the minority strategy. This setting permits distinguishing between irrational herding and rational self-interesta fundamental challenge ...Working Paper -
Morphometry and mechanical instability at the onset of epithelial bladder cancer
(2023)bioRxivMalignancies of epithelial tissues, called carcinomas, account for the majority of cancer cases. Much cancer research has focused on genetic alterations and their relation to different carcinoma phenotypes. Besides a rewiring in the signalling networks, carcinoma progression is accompanied by mechanical changes in the epithelial cells and the extracellular matrix. Here, we reveal intricate morphologies in the basement membrane at the onset ...Working Paper -
Tracing the Footsteps of Ideas: Time-respecting Paths Reveal Key Reformers and Communication Pathways in Protestant Letter Networks
(2023)SocArXivThe transmission of ideas plays a vital role in shaping society, fostering critical thinking, driving innovation, and facilitating cultural development. Previous studies have predominantly employed aggregated networks to investigate how ideas propagate through interactions and relationships among individuals. However, these approaches overlook the temporal ordering of interactions, distorting topological network measures and potentially ...Working Paper -
A new theoretical framework jointly explains behavioral and neural variability across subjects performing flexible decision-making
(2022)bioRxivThe ability to flexibly select and accumulate relevant information to form decisions, while ignoring irrelevant information, is a fundamental component of higher cognition. Yet its neural mechanisms remain unclear. Here we demonstrate that, under assumptions supported by both monkey and rat data, the space of possible network mechanisms to implement this ability is spanned by the combination of three different components, each with specific ...Working Paper -
Comment on "A literature review and meta-analysis of the effects of lockdowns on COVID-19 mortality"
(2022)In a recent working paper, Herby et al. conduct a systematic review and meta-analysis of the effects of lockdowns on COVID-19 mortality. Based on their results, they conclude that "lockdowns have had little to no public health effects'' and that "lockdowns should be rejected out of hand as a pandemic policy instrument'' (p. 2). These strong conclusions have quickly been taken up by the public media. Here, we would like to comment on the ...Working Paper -
reComBat: Batch effect removal in large-scale, multi-source omics data integration
(2021)bioRxivWith the steadily increasing abundance of omics data produced all over the world, some-times decades apart and under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch effect removal for entire databases lies in the large number and coincide of both batches and desired, biological variation resulting in ...Working Paper -
B cell clonal expansion is correlated with antigen-specificity in young but not old mice
(2021)bioRxivAging of the humoral immune response has been shown to affect its critical role in defending the host from a variety of pathogens. Technical limitations have nevertheless made it challenging to investigate the relationship between genotype and phenotype of antibody repertoires in the context of aging. We therefore performed single-cell sequencing of over 95,000 B cells to simultaneously investigate B cell receptor (BCR) repertoires and ...Working Paper -
High-throughput identification of RNA localization elements reveals a regulatory role for A/G rich sequences
(2021)bioRxivHundreds of RNAs are enriched in the projections of neuronal cells. For the vast majority of them, though, the sequence elements within them that regulate their localization are unknown. To identify RNA elements capable of directing transcripts to neurites, we designed and deployed a massively parallel reporter assay that tested the localization regulatory ability of thousands of sequence fragments drawn from endogenous mouse 3′ UTRs. We ...Working Paper -
The Physiological Landscape and Specificity of Antibody Repertoires
(2021)bioRxivDiverse antibody repertoires spanning multiple lymphoid organs (e.g., bone marrow, spleen, lymph nodes) form the foundation of protective humoral immunity. Changes in their composition across lymphoid organs are a consequence of B-cell selection and migration events leading to a highly dynamic and unique physiological landscape of antibody repertoires upon antigenic challenge (e.g., vaccination). However, to what extent B cells encoding ...Working Paper